Zzapper, I placed c:\cygwin\bin;C:\cygwin\usr\local\bin in my path and to timidity to work.
One small word of warning: there are tools out there (gaim, wincvs, etc.) that like to look for installed (non-cygwin) subsystems like TCL or Python by just doing a search for the appropriate DLL on the path (tcl84.dll, etc.).
If they find the Cygwin DLL instead, and try to load it, they'll hang.
(Normally, Cygwin DLLs are supposed to be named cygxxxx.dll (by convention), but TCL, Python, and a couple of others have not followed this convention, and are merrily tripping up non-Cygwin tools.)
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